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Early and Late Cretaceous alkaline and alkaline–carbonatitic complexes from southern Brazil are located along the main tectonic lineaments of the South America Platform. Calcium-, magnesium-, and ferrocarbonatites are well represented and frequently associated even in the same complex. Primary carbonates present significant variations in C–O isotopic compositions, which are mainly due to isotope exchange with H2O–CO2-rich hydrothermal fluids, whereas fractional crystallization or liquid immiscibility probably affects the δ18O and δ13C values by no more than 2δ‰. Our isotope exchange model implies that the most significant isotopic variations took place in a hydrothermal environment, e.g., in the range 400–80°C, involving fluids with the CO2/H2O ratio ranging from 0.8 to 1. Sr–Nd–Pb isotope systematics highlight heterogeneous mixtures between HIMU and EMI mantle components, similar to the associated alkaline rocks and the flood tholeiites from southern Brazil. In spite of the strong variation shown by C–O isotopes, Sr–Nd–Pb–Os isotopic systematics could be related to an isotopically enriched source where the chemical heterogeneities reflect a depleted mantle “metasomatized” by small-volume melts and fluids rich in incompatible elements. These fluids are expected to have promoted crystallization of K-rich phases in the mantle, which produced a veined network variously enriched in LILE and LREE. The newly formed veins (enriched component) and peridotite matrix (depleted component) underwent a different isotopic evolution with time as reflected by the carbonatites. These conclusions may be extended to the whole Paraná–Etendeka system, where isotopically distinct parent magmas were generated following two main enrichment events of the subcontinental lithospheric mantle at 2.0–1.4 and 1.0–0.5 Ga, respectively, as also supported by Re–Os systematics. The mantle sources preserved the isotopic heterogeneities over a long time, suggesting a nonconvective lithospheric mantle beneath different cratons or intercratonic regions. Overall, the data indicate that the alkaline–carbonatitic magmatism originated from a locally heterogeneous subcontinental mantle.